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Reading all the genes (exome) or the entire DNA (genome) of a tumour, rather than a chosen panel.
WGS reveals structural variants, mutational signatures (HRD, APOBEC, tobacco), whole-genome doubling, and non-coding drivers. Used by national programmes (Genomics England, Hartwig) and for neoantigen prediction in personalised vaccines. Long-read sequencing (PacBio, Oxford Nanopore) resolves complex rearrangements and methylation in one run.
Shotgun sequencing of the whole genome (or exon-captured fraction) at 30-100x depth, tumour-normal paired.
Dependencies are what this technology cannot be delivered without: manufacturing steps, instruments, software, upstream methods. See its full chain on the map.
The first FDA-approved test that sequences all of a tumour's genes and gene activity at once, used to match patients to several targeted drugs.
The 48 most recent of 68 papers; see them all →
If a childhood exposure to colibactin-producing Escherichia coli writes APC mutations into the colon decades before a tumour appears, then the rise in early-onset bowel cancer may be preventable by something done in childhood rather than by screening alone.
For the first time a randomised trial suggests that a vaccine tailored to an individual's tumour can reduce relapse when combined with immunotherapy, which is a proof of concept for a field that had failed for decades. Nothing changes for patients yet: the trial was small, the confidence interval crossed one, and the phase 3 trial in melanoma (and parallel trials in lung and other cancers) must confirm it. If it does, personalised mRNA vaccines could become a routine adjunct to checkpoint inhibitors after surgery.
It is the positive half of the tumour mutational burden story and it applies only to single-agent immunotherapy, which is the setting fewest patients are treated in.
This is the result that ended tumour mutational burden as a practical selector in lung cancer: in the regimen most patients receive, it selects nobody, and neither do the co-mutations most often quoted as reasons to withhold immunotherapy.
Relapse after surgery is driven by particular subclones that can be identified in the primary tumour and tracked in blood, which argues for evolution-aware adjuvant strategies. The pollution finding reframes carcinogenesis: some agents promote already-mutant cells rather than causing mutations.
Lung cancer in never-smokers is not smokers' lung cancer with the smoking removed; it is a different set of diseases with a different clock. The slow-growing piano subtype in particular is the argument that a screening test aimed at never-smokers would need to look for something other than what low-dose computed tomography was built to find.
The piece that turns a research classification into something a trial can use on one person's biopsy, with a probability attached rather than a flat label. It is the reason genetics-directed lymphoma trials became possible at all.
It gives surveillance a target and a timetable: catch high-grade dysplasia and there are about three years before invasion, and TGF-beta pathway loss is the event to detect.
Query for this technology: (TITLE:"whole-genome sequencing" OR ABSTRACT:"whole-genome sequencing" OR TITLE:"whole genome sequencing" OR ABSTRACT:"whole genome sequencing" OR TITLE:"whole-exome sequencing" OR ABSTRACT:"whole-exome sequencing") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Whole-exome & whole-genome sequencing, not a curated reading list.
Shares Isabl, BostonGene, Carlos Caldas, Genomics-driven precision medicine for advanced pancreatic cancer: early results from the COMPASS trial.
Shares A standard evolvability score for every tumour, A single calibrated tumour mutational burden across all sequencing panels, Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer, The landscape of somatic mutation in normal colorectal epithelial cells.
Shares A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns, Genomic correlates of clinical outcome in advanced prostate cancer, Mutational signatures associated with tobacco smoking in human cancer, Clonal history and genetic predictors of transformation into small-cell carcinomas from lung adenocarcinomas.
Shares The landscape of somatic mutation in normal colorectal epithelial cells, Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer, Genomic correlates of clinical outcome in advanced prostate cancer, Whole-genome and transcriptome sequencing of prostate cancer identifies new genetic alterations driving disease progression.
Shares A standard evolvability score for every tumour, BostonGene, Valius Sciences, NHS Genomic Medicine Service.
Shares Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer, Genomic correlates of immune-cell infiltrates in colorectal carcinoma, Association of distinct mutational signatures with correlates of increased immune activity in pancreatic ductal adenocarcinoma, Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer.
Shares Gad Getz, Pool every multi-sample tumour genome into one open evolution atlas, Catherine J. Wu, Let patients themselves donate their records and samples for ultra-rare cancers.
Shares Pool every multi-sample tumour genome into one open evolution atlas, BostonGene, Link every national cancer registry to tumour genomics, Bank three spatially separate tumour blocks from every resection.
Open-source projects that implement or serve this technology, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
The Broad Institute's Genome Analysis Toolkit: variant discovery for germline and somatic DNA, including the Mutect2 somatic caller and copy-number tools most cancer pipelines start from.
A community Nextflow pipeline for germline and somatic variant calling on whole-genome and exome data, with tumour-normal pairs, several callers and annotation built in.
The Hartwig Medical Foundation's whole-genome cancer analysis suite: purity and ploidy (PURPLE), structural variants (GRIDSS, LINX), point mutations (SAGE) and reporting, run on thousands of Dutch tumours.
A Nextflow pipeline that runs the Hartwig hmftools cancer analysis stack end to end on whole-genome and transcriptome data.
The Sanger Cancer Genome Project's whole-genome tumour-normal pipeline packaged as a container for Dockstore.
The Myeloma Genome Project's whole-genome pipeline for a thousand multiple myeloma patients.
Memorial Sloan Kettering's Nextflow pipeline for whole-exome and whole-genome tumour-normal analysis.
Commercial and regulated products that serve this technology. Each card says what is behind it: a regulator's database, the literature, a public body's list, or only the company's own words. Listing is not endorsement, and a clearance is a regulatory fact, not a clinical one.
A hospital's own targeted sequencing test and its analysis pipeline, authorised in the United States and the source of one of the largest public clinical sequencing cohorts.
Hardware-accelerated secondary analysis: alignment and variant calling on a field-programmable gate array, which is how many clinical laboratories keep up with their sequencers.
Reimplementations of the standard variant calling pipelines, including the somatic ones, engineered to give the same answers much faster on ordinary hardware.
Open-source software, hardware and data projects catalogued by a third party, the Open Medical Registry, that bear on this technology. Listing is not endorsement; check each project's own licence and validation before clinical use.
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other...
ClairS: a deep-learning method for long-read tumor, normal pair somatic small variant calling
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Official code repository for GATK versions 4 and up
A structural variation pipeline for short-read sequencing
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
From the Open Medical Registry (openmedical.sh), an MIT-licensed catalogue of open-source medicine. Blurbs are one line from each registry record; every project keeps its own licence.